diff options
Diffstat (limited to 'uploader/templates/species')
| -rw-r--r-- | uploader/templates/species/base.html | 5 | ||||
| -rw-r--r-- | uploader/templates/species/create-species.html | 112 | ||||
| -rw-r--r-- | uploader/templates/species/list-species.html | 2 | ||||
| -rw-r--r-- | uploader/templates/species/macro-display-species-card.html | 47 | ||||
| -rw-r--r-- | uploader/templates/species/macro-select-species.html | 85 | ||||
| -rw-r--r-- | uploader/templates/species/sui-base.html | 10 | ||||
| -rw-r--r-- | uploader/templates/species/sui-view-species.html | 127 | ||||
| -rw-r--r-- | uploader/templates/species/view-species.html | 6 |
8 files changed, 307 insertions, 87 deletions
diff --git a/uploader/templates/species/base.html b/uploader/templates/species/base.html index 04391db..f64f72b 100644 --- a/uploader/templates/species/base.html +++ b/uploader/templates/species/base.html @@ -6,7 +6,12 @@ {%else%} class="breadcrumb-item" {%endif%}> + {%if species is mapping%} + <a href="{{url_for('species.view_species', species_id=species.SpeciesId)}}"> + {{species.Name}}</a> + {%else%} <a href="{{url_for('species.list_species')}}">Species</a> + {%endif%} </li> {%block lvl2_breadcrumbs%}{%endblock%} {%endblock%} diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html index 0d0bedf..138dbaa 100644 --- a/uploader/templates/species/create-species.html +++ b/uploader/templates/species/create-species.html @@ -19,72 +19,88 @@ <div class="row"> <form id="frm-create-species" method="POST" - action="{{url_for('species.create_species')}}"> + action="{{url_for('species.create_species', return_to=return_to)}}" + class="form-horizontal"> <legend>Create Species</legend> {{flash_all_messages()}} + <input type="hidden" name="return_to" value="{{return_to}}"> + <div class="form-group"> - <label for="txt-taxonomy-id" class="form-label"> + <label for="txt-taxonomy-id" class="control-label col-sm-2"> Taxonomy ID</label> - <div class="input-group"> - <input id="txt-taxonomy-id" - name="species_taxonomy_id" - type="text" - class="form-control" /> - <span class="input-group-btn"> - <button id="btn-search-taxonid" class="btn btn-info">Search</button> - </span> + <div class="col-sm-10"> + <div class="input-group"> + <input id="txt-taxonomy-id" + name="species_taxonomy_id" + type="text" + class="form-control" /> + <span class="input-group-btn"> + <button id="btn-search-taxonid" class="btn btn-info">Search</button> + </span> + </div> + <small class="form-text text-small text-muted"> + Use + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/" + title="NCBI's Taxonomy Browser homepage" + target="_blank"> + NCBI's Taxonomy Browser homepage</a> to search for the species you + want. If the species exists on NCBI, they will have a Taxonomy ID. Copy + that Taxonomy ID to this field, and click "Search" to auto-fill the + details.<br /> + This field is optional.</small> </div> - <small class="form-text text-small text-muted">Provide the taxonomy ID for - your species that can be used to link to external sites like NCBI. Enter - the taxonomy ID and click "Search" to auto-fill the form with data. - <br /> - While it is recommended to provide a value for this field, doing so is - optional. - </small> </div> <div class="form-group"> - <label for="txt-species-name" class="form-label">Common Name</label> - <input id="txt-species-name" - name="common_name" - type="text" - class="form-control" - required="required" /> - <small class="form-text text-muted">Provide the common, possibly - non-scientific name for the species here, e.g. Human, Mouse, etc.</small> + <label for="txt-species-name" class="control-label col-sm-2">Common Name</label> + <div class="col-sm-10"> + <input id="txt-species-name" + name="common_name" + type="text" + class="form-control" + required="required" /> + <small class="form-text text-muted">This is the day-to-day term used by + laymen, e.g. Mouse (instead of Mus musculus), round worm (instead of + Ascaris lumbricoides), etc.<br /> + For species without this, just enter the scientific name. + </small> + </div> </div> <div class="form-group"> - <label for="txt-species-scientific" class="form-label"> + <label for="txt-species-scientific" class="control-label col-sm-2"> Scientific Name</label> - <input id="txt-species-scientific" - name="scientific_name" - type="text" - class="form-control" - required="required" /> - <small class="form-text text-muted">Provide the scientific name for the - species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small> + <div class="col-sm-10"> + <input id="txt-species-scientific" + name="scientific_name" + type="text" + class="form-control" + required="required" /> + <small class="form-text text-muted">This is the scientific name for the + species e.g. Homo sapiens, Mus musculus, etc.</small> + </div> </div> <div class="form-group"> - <label for="select-species-family" class="form-label">Family</label> - <select id="select-species-family" - name="species_family" - required="required" - class="form-control"> - <option value="">Please select a grouping</option> - {%for family in families%} - <option value="{{family}}">{{family}}</option> - {%endfor%} - </select> - <small class="form-text text-muted"> - This is a generic grouping for the species that determines under which - grouping the species appears in the GeneNetwork menus</small> + <label for="select-species-family" class="control-label col-sm-2">Family</label> + <div class="col-sm-10"> + <select id="select-species-family" + name="species_family" + required="required" + class="form-control"> + <option value="ungrouped">I do not know what to pick</option> + {%for family in families%} + <option value="{{family}}">{{family}}</option> + {%endfor%} + </select> + <small class="form-text text-muted"> + This is a rough grouping of the species.</small> + </div> </div> - <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> <input type="submit" value="create new species" class="btn btn-primary" /> @@ -113,7 +129,7 @@ } msg = ( "Request to '${uri}' failed with message '${textStatus}'. " - + "Please try again later, or fill the details manually."); + + "Please try again later, or fill the details manually."); alert(msg); console.error(msg, data, textStatus); return false; diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html index 85c9d40..64084b0 100644 --- a/uploader/templates/species/list-species.html +++ b/uploader/templates/species/list-species.html @@ -29,7 +29,7 @@ <caption>Available Species</caption> <thead> <tr> - <th>#</td> + <th></td> <th title="A common, layman's name for the species.">Common Name</th> <th title="The scientific name for the species">Organism Name</th> <th title="An identifier for the species in the NCBI taxonomy database"> diff --git a/uploader/templates/species/macro-display-species-card.html b/uploader/templates/species/macro-display-species-card.html index 857c0f0..30c564f 100644 --- a/uploader/templates/species/macro-display-species-card.html +++ b/uploader/templates/species/macro-display-species-card.html @@ -3,14 +3,49 @@ <div class="card-body"> <h5 class="card-title">Species</h5> <div class="card-text"> - <dl> - <dt>Common Name</dt> - <dd>{{species.SpeciesName}}</dd> + <table class="table"> + <tbody> + <tr> + <td>Common Name</td> + <td>{{species.SpeciesName}}</td> + </tr> - <dt>Scientific Name</dt> - <dd>{{species.FullName}}</dd> - </dl> + <tr> + <td>Scientific Name</td> + <td>{{species.FullName}}</td> + </tr> + </tbody> + </table> </div> </div> </div> {%endmacro%} + + +{%macro display_sui_species_card(species)%} +<div class="row"> + <table class="table"> + <caption>Current Species</caption> + <tbody> + <tr> + <th>Name</th> + <td>{{species["Name"] | title}}</td> + </tr> + <tr> + <th>Scientific</th> + <td>{{species["FullName"]}}</td> + </tr> + {%if species["TaxonomyId"]%} + <tr> + <th>Taxonomy ID</th> + <td> + <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={{species.TaxonomyId}}" + title="NCBI's Taxonomy Browser page for {{species.Name}}"> + {{species.TaxonomyId}}</a> + </td> + </tr> + </tbody> + {%endif%} + </table> +</div> +{%endmacro%} diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html index 6955134..3714ae4 100644 --- a/uploader/templates/species/macro-select-species.html +++ b/uploader/templates/species/macro-select-species.html @@ -1,38 +1,59 @@ +{%from "macro-step-indicator.html" import step_indicator%} + {%macro select_species_form(form_action, species)%} -{%if species | length > 0%} -<form method="GET" action="{{form_action}}"> - <legend>Select Species</legend> - - <div class="form-group"> - <label for="select-species" class="form-label">Species</label> - <select id="select-species" - name="species_id" - class="form-control" - required="required"> - <option value="">Select Species</option> - {%for group in species%} - {{group}} - <optgroup {%if group[0][1] is not none%} - label="{{group[0][1].capitalize()}}" - {%else%} - label="Undefined" - {%endif%}> - {%for aspecies in group[1]%} - <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> - {%endfor%} - </optgroup> - {%endfor%} - </select> +<form method="GET" action="{{form_action}}" class="form-horizontal"> + + <h2>{{step_indicator("1")}} What species do you want to work with?</h2> + + {%if species | length != 0%} + + <p class="form-text">Search for, and select the species from the table below + and click "Continue"</p> + + <div class="radio"> + <label for="rdo-cant-find-species" + style="font-weight: 1;"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + I could not find the species I want (create it). + </label> </div> - <div class="form-group"> - <input type="submit" value="Select" class="btn btn-primary" /> + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary" + value="continue" /> </div> + + <div style="margin-top:3em;"> + <table id="tbl-select-species" class="table compact stripe" + data-species-list='{{species | tojson}}'> + <div class=""> + <thead> + <tr> + <th></th> + <th>Species Name</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> + + {%else%} + + <label class="control-label" for="rdo-cant-find-species"> + <input id="rdo-cant-find-species" type="radio" name="species_id" + value="CREATE-SPECIES" /> + There are no species to select from. Create the first one.</label> + + <div class="col-sm-offset-10 col-sm-2"> + <input type="submit" + class="btn btn-primary col-sm-offset-1" + value="continue" /> + </div> + + {%endif%} + </form> -{%else%} -<p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-mark"></span> - We could not find species to select from! -</p> -{%endif%} {%endmacro%} diff --git a/uploader/templates/species/sui-base.html b/uploader/templates/species/sui-base.html new file mode 100644 index 0000000..f7b4fef --- /dev/null +++ b/uploader/templates/species/sui-base.html @@ -0,0 +1,10 @@ +{%extends "sui-base.html"%} + +{%block breadcrumbs%} +{{super()}} +<li class="breadcrumb-item"> + <a href="{{url_for('species.view_species', species_id=species['SpeciesId'])}}"> + {{species["Name"]|title}} + </a> +</li> +{%endblock%} diff --git a/uploader/templates/species/sui-view-species.html b/uploader/templates/species/sui-view-species.html new file mode 100644 index 0000000..4b6402e --- /dev/null +++ b/uploader/templates/species/sui-view-species.html @@ -0,0 +1,127 @@ +{%extends "species/sui-base.html"%} +{%from "flash_messages.html" import flash_all_messages%} +{%from "macro-forms.html" import add_http_feature_flags%} +{%from "macro-step-indicator.html" import step_indicator%} +{%from "species/macro-display-species-card.html" import display_sui_species_card%} + +{%block title%}View Species{%endblock%} + +{%macro add_form_buttons()%} +<div class="row form-buttons"> + <div class="col"> + <input type="submit" + value="use selected population" + class="btn btn-primary" /> + </div> + + <div class="col"> + <a href="url_for('species.population.create_population', + species_id=species.SpeciesId, + return_to='species.view_species')" + title="Create a new population for species '{{species.Name}}'." + class="btn btn-outline-info"> + Create a new population + </a> + </div> +</div> +{%endmacro%} + + +{%block contents%} +<div class="row"> + <h2 class="heading">{{species.FullName}} ({{species.Name}})</h2> +</div> + +<div class "row"> + <ul class="nav nav-tabs" id="species-actions"> + <li class="nav-item presentation"> + <button class="nav-link active" + id="populations-tab" + data-bs-toggle="tab" + data-bs-target="#populations-content" + type="button" + role="tab" + aria-controls="populations-content" + aria-selected="true">Populations</button> + </li> + <li class="nav-item presentation"> + <button class="nav-link" + id="sequencing-platforms-tab" + data-bs-toggle="tab" + data-bs-target="#sequencing-platforms-content" + type="button" + role="tab" + aria-controls="sequencing-platforms-content" + aria-selected="true">Sequencing Platforms</button> + </li> + </ul> +</div> + +<div class="row"> + <div class="tab-content" id="species-tabs-content"> + <div class="tab-pane fade show active" + id="populations-content" + role="tabpanel" + aria-labelledby="populations-content-tab"> + <p>Data belonging to a particular species is further divided into one or more + populations for easier handling. Please select the population you want to work + with.</p> + + <form method="GET" + action="{{url_for('species.view_species', species_id=species.SpeciesId)}}" + class="form-horizontal"> + {{add_http_feature_flags()}} + {{add_form_buttons()}} + + {%if populations | length != 0%} + <div style="margin-top:0.3em;"> + <table id="tbl-select-population" class="table compact stripe" + data-populations-list='{{populations | tojson}}'> + <thead> + <tr> + <th></th> + <th>Population</th> + </tr> + </thead> + + <tbody></tbody> + </table> + </div> + + {%else%} + <p class="form-text"> + There are no populations currently defined for {{species['FullName']}} + ({{species['SpeciesName']}}).</p> + {%endif%} + + {{add_form_buttons()}} + + </form> + </div> + <div class="tab-pane fade" + id="sequencing-platforms-content" + role="tabpanel" + aria-labelledby="sequencing-platforms-content-tab"> + <p>Upload and manage the sequencing platforms for species + '{{species.Name | title}} ({{species.FullName}})' + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId)}}" + title="Manage sequencing platforms for {{species.Name}}">here</a>. + </p> + </div> + </div> +</div> +{%endblock%} + +{%block sidebarcontents%} +<div class="row"> + <p>You can manage species' populations and sequencing platforms here. Select + the tab for the feature you wish to continue working on.</p> +</div> +{{display_sui_species_card(species)}} +{%endblock%} + + +{%block javascript%} +<script type="text/javascript" src="/static/js/populations.js"></script> +{%endblock%} diff --git a/uploader/templates/species/view-species.html b/uploader/templates/species/view-species.html index b01864d..2d02f7e 100644 --- a/uploader/templates/species/view-species.html +++ b/uploader/templates/species/view-species.html @@ -45,6 +45,12 @@ title="Create/Edit populations for {{species.FullName}}"> Manage populations</a> </li> + <li> + <a href="{{url_for('species.platforms.list_platforms', + species_id=species.SpeciesId)}}" + title="Create/Edit sequencing platforms for {{species.FullName}}"> + Manage sequencing platforms</a> + </li> </ol> |